DOCSLIB.ORG

Impact of the Post-Transplant Period and Lifestyle Diseases on Human Gut Microbiota in Kidney Graft Recipients

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Impact of the Post-Transplant Period and Lifestyle Diseases on Human Gut Microbiota in Kidney Graft Recipients microorganisms Article Impact of the Post-Transplant Period and Lifestyle Diseases on Human Gut Microbiota in Kidney Graft Recipients Nessrine Souai 1,2 , Oumaima Zidi 1,2 , Amor Mosbah 1, Imen Kosai 3, Jameleddine El Manaa 3, Naima Bel Mokhtar 4, Elias Asimakis 4 , Panagiota Stathopoulou 4 , Ameur Cherif 1 , George Tsiamis 4 and Soumaya Kouidhi 1,* 1 Laboratory of Biotechnology and Valorisation of Bio-GeoRessources, Higher Institute of Biotechnology of Sidi Thabet, BiotechPole of Sidi Thabet, University of Manouba, Ariana 2020, Tunisia; [email protected] (N.S.); [email protected] (O.Z.); [email protected] (A.M.); [email protected] (A.C.) 2 Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, Farhat Hachad Universitary Campus, Rommana 1068, Tunis, Tunisia 3 Unit of Organ Transplant Military Training Hospital, Mont Fleury 1008, Tunis, Tunisia; [email protected] (I.K.); [email protected] (J.E.M.) 4 Laboratory of Systems Microbiology and Applied Genomics, Department of Environmental Engineering, University of Patras, 2 Seferi St, 30100 Agrinio, Greece; [email protected] (N.B.M.); [email protected] (E.A.); [email protected] (P.S.); [email protected] (G.T.) * Correspondence: [email protected]; Tel.: +216-95-694-135 Received: 8 September 2020; Accepted: 30 October 2020; Published: 4 November 2020 Abstract: Gaining long-term graft function and patient life quality remain critical challenges following kidney transplantation. Advances in immunology, gnotobiotics, and culture-independent molecular techniques have provided growing insights into the complex relationship of the microbiome and the host. However, little is known about the over time-shift of the gut microbiota in the context of kidney transplantation and its impact on both graft and health stability. Here we aimed to characterize the structure of gut microbiota within stable kidney graft recipients. We enrolled forty kidney transplant patients after at least three months of transplantation and compared them to eighteen healthy controls. The overall microbial community structure of the kidney transplanted group was clearly different from control subjects. We found lower relative abundances of Actinobacteria, Bacteroidetes, and Verrucomicrobia within the patient group and a higher abundance of Proteobacteria compared to the control group. Both richness and Shannon diversity indexes were significantly lower in the kidney graft recipients than in healthy controls. Post-graft period was positively correlated with the relative abundance of the Proteobacteria phylum, especially Escherichia.Shigella genus. Interestingly, only Parabacteroides was found to significantly differentiate patients that were not suffering from lifestyle diseases and those who suffer from post-graft complications. Furthermore, network analysis showed that the occurrence of lifestyle diseases was significantly linked with a higher number of negative interactions of Sutterella and Succinivibrio genera within patients. This study characterizes gut microbiome fluctuation in stable kidney transplant patients after a long post-allograft period. Analysis of fecal microbiota could be useful for nephrologists as a new clinical tool that can improve kidney allograft monitoring and outcomes. Keywords: 16S rRNA gene; amplicon sequencing; dysbiosis; bioinformatics; kidney transplantation Microorganisms 2020, 8, 1724; doi:10.3390/microorganisms8111724 www.mdpi.com/journal/microorganisms Microorganisms 2020, 8, 1724 2 of 19 1. Introduction Increasing kidney disease and subsequent chronic kidney disease (CKD) is related to the ageing society and high morbidity due to lifestyle diseases such as diabetes, atherosclerosis, and hypertension [1]. During the past decade, kidney transplantation was increasingly recognized as the treatment of choice for medically suitable patients with CKD [2]. As well as improving quality of life, successful transplantation confers significant benefits by improving the morbidity and mortality of CKD patients who receive kidney transplant over those who undergo dialysis [3]. The clinical concern of the successful transplant patient is rejection. At five-years posttransplant, kidney allograft survival is as low as 71% [4]. Standards of care protocols recommend regular surveillance for detecting and treating early rejection, which is done by checking creatinine and urine proteinuria and/or by routine biopsy at regular posttransplant intervals [5]. However, a recent study proved that 41.3% of kidney recipients have been receiving low-value, unnecessary biopsies [6]. This evidence suggests that better diagnostic, non-invasive tools may be more effective than invasive, costly biopsies in the context of predicting kidney rejection. In addition, dosing of immunosuppressors to establish therapeutic levels in recipients of organ transplants remains a challenging task because of high interpatient and intrapatient variability in drug metabolism. Tacrolimus possesses a narrow therapeutic index with sub-therapeutic levels leading to immune rejection and supra-therapeutic levels that could lead to nephrotoxicity and neurotoxicity [7]. Altogether, these studies suggest that nephrologists and transplant patients need better tests than creatinine and proteinuria and less invasive approaches than routine biopsies to determine when transplant patients should be investigated for rejection and immunosuppressive treatment. Both human and mouse studies reported that the gut microbial community is associated with complications in kidney allograft recipients, including overall survival, infections, and graft rejection [8,9]. Growing evidence suggests that the gut microbiota serves as both the origin and the target of post-transplant complications. Several factors pre-, intra-, and/or post-transplantation can result in an altered microbiome and consequent dysbiosis. These factors include the use of antimicrobials and immunosuppressant drugs, hemodialysis, and the new post-surgical anatomy. Dysbiosis may lead to several post-transplantation complications such as the risk of infection (urinary tract infection, infectious diarrhea), adverse immunologic phenomena (autoimmune hemolytic anemia), graft rejection, and increased mortality rates. Selectively avoiding these alterations and inducing eubiotic changes in the peri-transplantation setting may hold preventative and therapeutic potential [10]. Additionally, the microbiota has been found to modulate drug pharmacokinetics and accordingly, therapeutic response. Of interest, deep sequencing identified that the abundance of Faecalibacterium prausnitzii in feces early after kidney transplantation is associated with tacrolimus dosing requirements in kidney transplant recipients [11]. Furthermore, some studies investigated the potential of intestinal microbial flora as microbial biomarkers for the non-invasive diagnosis and selection of appropriate personalized treatment for CKD [12]. However, it remains unclear which bacterial genera are optimal to predict post graft complications in the kidney transplant population. Therefore, this study was performed in order to identify and understand changes in gut microbial composition between stable kidney transplant patients and healthy controls. 2. Materials and Methods 2.1. Study Cohort With the approval of the Tunisian Military University hospital’s ethics committee, we enrolled forty renal transplant recipients for a fecal specimen collection and clinical data study. The subjects provided the fecal specimens within one day of production, and the samples were frozen at 80 C. − ◦ Similarly, stool samples were collected from (n = 18) healthy subjects and written informed consent was obtained for each enrollee. Microorganisms 2020, 8, 1724 3 of 19 In order to investigate the variability in fecal gut microbiota over time, we divided the study cohort into three subgroups according to the graft stability state: short post-graft period (“SG”: from 3 months to 1 year; n = 11), medium-length post-graft period (“MG” from 1 year to 10 years; n = 20), and long post-transplant period (“LG” from 10 to 22 years n = 9). These three subgroups were compared to the healthy control samples (n = 18). We conducted further analysis of the fecal specimens based on the health status of the participants and whether or not they suffer from any lifestyle diseases that were named associated diseases (ADs). In the present study, n = 24 patients suffered from one or multiple complications from the following list: obesity, diabetes, high blood pressure, and dyslipidemia. However, n = 16 were kidney graft recipients that did not suffer from other associated diseases. Age and gender factors were also investigated but not reported in the present study for non-significance. This could be due to the small number of subjects covering a broad range of ages. The study was conducted according to the principles expressed in the Declaration of Helsinki, and all research procedures were approved on 5 March 2018 by the Bioethics Committee of the Military University Hospital of Tunis (No. 05032018). 2.2. DNA Extraction, First-Step PCR Amplification and Purification Total genomic DNA was isolated from the fecal specimens using an InnuPREP DNA kit (Analytik Jena, Jena, Germany) according to the manufacturer’s instructions. Three replicates of each sample were extracted. The quality and quantity of DNA samples were tested using a Q5000 micro-volume UV–Vis spectrophotometer (Quawell Technology, San Jose, CA, USA). DNA
Load more

Recommended publications
  • Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis
    International Journal of Molecular Sciences Review Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis David Johane Machate 1, Priscila Silva Figueiredo 2 , Gabriela Marcelino 2 , Rita de Cássia Avellaneda Guimarães 2,*, Priscila Aiko Hiane 2 , Danielle Bogo 2, Verônica Assalin Zorgetto Pinheiro 2, Lincoln Carlos Silva de Oliveira 3 and Arnildo Pott 1 1 Graduate Program in Biotechnology and Biodiversity in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] (D.J.M.); [email protected] (A.P.) 2 Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; pri.fi[email protected] (P.S.F.); [email protected] (G.M.); [email protected] (P.A.H.); [email protected] (D.B.); [email protected] (V.A.Z.P.) 3 Chemistry Institute, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +55-67-3345-7416 Received: 9 March 2020; Accepted: 27 March 2020; Published: 8 June 2020 Abstract: Long-term high-fat dietary intake plays a crucial role in the composition of gut microbiota in animal models and human subjects, which affect directly short-chain fatty acid (SCFA) production and host health. This review aims to highlight the interplay of fatty acid (FA) intake and gut microbiota composition and its interaction with hosts in health promotion and obesity prevention and its related metabolic dysbiosis.
    [Show full text]
  • Effect of Vertical Flow Exchange on Microbial Community Dis- Tributions in Hyporheic Zones
    Article 1 by Heejung Kim and Kang-Kun Lee* Effect of vertical flow exchange on microbial community dis- tributions in hyporheic zones School of Earth and Environmental Sciences, Seoul National University, Seoul 08826, Republic of Korea; *Corresponding author, E-mail: [email protected] (Received: November 2, 2018; Revised accepted: January 6, 2019) https://doi.org/10.18814/epiiugs/2019/019001 The effect of the vertical flow direction of hyporheic flux advance of hydrodynamic modeling has improved research of hydro- on the bacterial community is examined. Vertical velocity logical exchange processes at the hyporheic zone (Cardenas and Wil- change of the hyporheic zone was examined by installing son, 2007; Fleckenstein et al., 2010; Endreny et al., 2011). Also, this a piezometer on the site, and a total of 20,242 reads were zone has plentiful micro-organisms. The hyporheic zone constituents analyzed using a pyrosequencing assay to investigate the a dynamic hotspot (ecotone) where groundwater and surface water diversity of bacterial communities. Proteobacteria (55.1%) mix (Smith et al., 2008). were dominant in the hyporheic zone, and Bacteroidetes This area constitutes a flow path along which surface water down wells into the streambed sediment and groundwater up wells in the (16.5%), Actinobacteria (7.1%) and other bacteria phylum stream, travels for some distance before eventually mixing with (Firmicutes, Cyanobacteria, Chloroflexi, Planctomycetesm groundwater returns to the stream channel (Hassan et al., 2015). Sur- and unclassified phylum OD1) were identified. Also, the face water enters the hyporheic zone when the vertical hydraulic head hyporheic zone was divided into 3 points – down welling of surface water is greater than the groundwater (down welling).
    [Show full text]
  • Exploring Salivary Microbiota in AIDS Patients with Different Periodontal Statuses Using 454 GS-FLX Titanium Pyrosequencing
    ORIGINAL RESEARCH published: 02 July 2015 doi: 10.3389/fcimb.2015.00055 Exploring salivary microbiota in AIDS patients with different periodontal statuses using 454 GS-FLX Titanium pyrosequencing Fang Zhang 1 †, Shenghua He 2 †, Jieqi Jin 1, Guangyan Dong 1 and Hongkun Wu 3* 1 State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, China, 2 Public Health Clinical Center of Chengdu, Chengdu, China, 3 Department of Geriatric Dentistry, West China College of Stomatology, Sichuan University, Chengdu, China Patients with acquired immunodeficiency syndrome (AIDS) are at high risk of opportunistic infections. Oral manifestations have been associated with the level of immunosuppression, these include periodontal diseases, and understanding the microbial populations in the oral cavity is crucial for clinical management. The aim of this study was to examine the salivary bacterial diversity in patients newly admitted to the AIDS ward of the Public Health Clinical Center (China). Saliva samples were Edited by: Saleh A. Naser, collected from 15 patients with AIDS who were randomly recruited between December University of Central Florida, USA 2013 and March 2014. Extracted DNA was used as template to amplify bacterial Reviewed by: 16S rRNA. Sequencing of the amplicon library was performed using a 454 GS-FLX J. Christopher Fenno, University of Michigan, USA Titanium sequencing platform. Reads were optimized and clustered into operational Nick Stephen Jakubovics, taxonomic units for further analysis. A total of 10 bacterial phyla (106 genera) were Newcastle University, UK detected. Firmicutes, Bacteroidetes, and Proteobacteria were preponderant in the *Correspondence: salivary microbiota in AIDS patients. The pathogen, Capnocytophaga sp., and others Hongkun Wu, Department of Geriatric Dentistry, not considered pathogenic such as Neisseria elongata, Streptococcus mitis, and West China College of Stomatology, Mycoplasma salivarium but which may be opportunistic infective agents were detected.
    [Show full text]
  • Microbes from Sequencing 16S Ribosomal DNA and Internal Transcribed Spacer 2 Cancan Cheng†, Jingjing Sun†, Fen Zheng, Kuihai Wu and Yongyu Rui*
    Cheng et al. Annals of Clinical Microbiology and Antimicrobials 2014, 13:1 http://www.ann-clinmicrob.com/content/13/1/1 RESEARCH Open Access Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2 Cancan Cheng†, Jingjing Sun†, Fen Zheng, Kuihai Wu and Yongyu Rui* Abstract Background: Clinical microbiology laboratories have to accurately identify clinical microbes. However, some isolates are difficult to identify by the automated biochemical text platforms, which are called “difficult-to-identify” microbes in this study. Therefore, the ability of 16S ribosomal DNA (16S rDNA) and internal transcribed spacer 2 (ITS2) sequencing to identify these “difficult-to-identify” bacteria and fungi was assessed in this study. Methods: Samples obtained from a teaching hospital over the past three years were examined. The 16S rDNA of four standard strains, 18 clinical common isolates, and 47 “difficult-to-identify” clinical bacteria were amplified by PCR and sequenced. The ITS2 of eight standard strains and 31 “difficult-to-identify” clinical fungi were also amplified by PCR and sequenced. The sequences of 16S rDNA and ITS2 were compared to reference data available in GenBank by using the BLASTN program. These microbes were identified according to the percentage of similarity to reference sequences of strains in GenBank. Results: The results from molecular sequencing methods correlated well with automated microbiological identification systems for common clinical isolates. Sequencing results of the standard strains were consistent with their known phenotype. Overall, 47 “difficult-to-identify” clinical bacteria were identified as 35 genera or species by sequence analysis (with 10 of these identified isolates first reported in clinical specimens in China and two first identified in the international literature).
    [Show full text]
  • 1 1 Children Developing Celiac Disease Have a Distinct And
    bioRxiv preprint doi: https://doi.org/10.1101/2020.02.29.971242; this version posted March 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 Children Developing Celiac Disease Have a Distinct and Proinflammatory Gut 3 Microbiota in the First 5 Years of Life 4 5 Qian Huang1, Yi Yang2, Vladimir Tolstikov3, Michael A. Kiebish3, Jonas F 6 Ludvigsson4,5, Noah W. Palm2, Johnny Ludvigsson6, Emrah Altindis1 7 8 9 Affiliations: 10 1 Boston College Biology Department, Chestnut Hill, MA 02467, USA 11 2 Department of Immunobiology, Yale University School of Medicine, New Haven, CT 12 06510, USA. 13 14 3 BERG, LLC, Framingham, MA, USA. 15 16 4 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17 Stockholm, Sweden 18 19 5 Department of Paediatrics, Örebro University Hospital, Sweden 20 6 Crown Princess Victoria's Children's Hospital, Region Östergötland, Division of 21 Pediatrics, Linköping University, Linköping, SE 58185, Sweden. 22 23 24 25 26 27 Correspondence to: Emrah Altindis, Boston College Biology Department, Higgins Hall, 28 140 Commonwealth Avenue Chestnut Hill, MA 02467. E-mail: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.29.971242; this version posted March 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 29 ABSTRACT 30 Objective: Celiac disease (CD) is an immune-mediated disease characterized by small intestinal 31 inflammation.
    [Show full text]
  • Effect of Dietary Fat on the Metabolism of Energy and Nitrogen, Serum
    bioRxiv preprint doi: https://doi.org/10.1101/438929; this version posted October 9, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Effect of Dietary Fat on the Metabolism of Energy and 2 Nitrogen, Serum Parameters, Rumen Fermentation, 3 and Microbiota in twin Hu Male Lambs 4 Wenjuan Lia, Hui Taoa, Naifeng Zhanga, Tao Maa, Kaidong Dengb, Biao Xiea, Peng Jiaa, Qiyu 5 Diaoa* 6 aFeed Research Institute, Key Laboratory of Feed Biotechnology of the Ministry of 7 Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China 8 bCollege of Animal Science, Jinling Institute of Technology, Nanjing, Jiangsu, China 9 *Corresponding author 10 E-mail:[email protected] 11 Abstract 12 Background: Fat is the main substance that provides energy to animals. However, 13 the use of fat in twin Hu lambs has not been investigated. Thirty pairs of male twin 14 lambs were examined to investigate the effects of dietary fat on the metabolism of 15 energy and nitrogen, ruminal fermentation, and microbial communities. The twins are 16 randomly allotted to two groups (high fat: HF, normal fat: NF). Two diets of equal 17 protein and different fat levels. The metabolism test was made at 50-60 days of age. 18 Nine pairs of twin lambs are slaughtered randomly, and the rumen fluid is collected at 19 60 days of age. 20 Results: The initial body weight (BW) in the HF group did not differ from that of NF 21 group (P > 0.05), but the final BW was tended to higher than that of NF group (0.05 < 22 P < 0.1).
    [Show full text]
  • Integrating Taxonomic, Functional, and Strain-Level Profiling of Diverse
    TOOLS AND RESOURCES Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 Francesco Beghini1†, Lauren J McIver2†, Aitor Blanco-Mı´guez1, Leonard Dubois1, Francesco Asnicar1, Sagun Maharjan2,3, Ana Mailyan2,3, Paolo Manghi1, Matthias Scholz4, Andrew Maltez Thomas1, Mireia Valles-Colomer1, George Weingart2,3, Yancong Zhang2,3, Moreno Zolfo1, Curtis Huttenhower2,3*, Eric A Franzosa2,3*, Nicola Segata1,5* 1Department CIBIO, University of Trento, Trento, Italy; 2Harvard T.H. Chan School of Public Health, Boston, United States; 3The Broad Institute of MIT and Harvard, Cambridge, United States; 4Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, San Michele all’Adige, Italy; 5IEO, European Institute of Oncology IRCCS, Milan, Italy Abstract Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and *For correspondence: phylogenetic profiling of metagenomes newly developed to build on the largest set of reference [email protected] (CH); sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of [email protected] (EAF); taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These [email protected] (NS) methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and †These authors contributed IBD (1635 metagenomes and 817 metatranscriptomes).
    [Show full text]
  • Bacterial Diversity and Functional Analysis of Severe Early Childhood
    www.nature.com/scientificreports OPEN Bacterial diversity and functional analysis of severe early childhood caries and recurrence in India Balakrishnan Kalpana1,3, Puniethaa Prabhu3, Ashaq Hussain Bhat3, Arunsaikiran Senthilkumar3, Raj Pranap Arun1, Sharath Asokan4, Sachin S. Gunthe2 & Rama S. Verma1,5* Dental caries is the most prevalent oral disease afecting nearly 70% of children in India and elsewhere. Micro-ecological niche based acidifcation due to dysbiosis in oral microbiome are crucial for caries onset and progression. Here we report the tooth bacteriome diversity compared in Indian children with caries free (CF), severe early childhood caries (SC) and recurrent caries (RC). High quality V3–V4 amplicon sequencing revealed that SC exhibited high bacterial diversity with unique combination and interrelationship. Gracillibacteria_GN02 and TM7 were unique in CF and SC respectively, while Bacteroidetes, Fusobacteria were signifcantly high in RC. Interestingly, we found Streptococcus oralis subsp. tigurinus clade 071 in all groups with signifcant abundance in SC and RC. Positive correlation between low and high abundant bacteria as well as with TCS, PTS and ABC transporters were seen from co-occurrence network analysis. This could lead to persistence of SC niche resulting in RC. Comparative in vitro assessment of bioflm formation showed that the standard culture of S. oralis and its phylogenetically similar clinical isolates showed profound bioflm formation and augmented the growth and enhanced bioflm formation in S. mutans in both dual and multispecies cultures. Interaction among more than 700 species of microbiota under diferent micro-ecological niches of the human oral cavity1,2 acts as a primary defense against various pathogens. Tis has been observed to play a signifcant role in child’s oral and general health.
    [Show full text]
  • Supplementary Figure Legends for Rands Et Al. 2019
    Supplementary Figure legends for Rands et al. 2019 Figure S1: Display of all 485 prophage genome maps predicted from Gram-Negative Firmicutes. Each horizontal line corresponds to an individual prophage shown to scale and color-coded for annotated phage genes according to the key displayed in the right- side Box. The left vertical Bar indicates the Bacterial host in a colour code. Figure S2: Projection of virome sequences from 183 human stool samples on A. Acidaminococcus intestini RYC-MR95, and B. Veillonella parvula UTDB1-3. The first panel shows the read coverage (Y-axis) across the complete Bacterial genome sequence (X-axis; with bp coordinates). Predicted prophage regions are marked with red triangles and magnified in the suBsequent panels. Virome reads projected outside of prophage prediction are listed in Table S4. Figure S3: The same display of virome sequences projected onto Bacterial genomes as in Figure S2, But for two different Negativicute species: A. Dialister Marseille, and B. Negativicoccus massiliensis. For non-phage peak annotations, see Table S4. Figure S4: Gene flanking analysis for the lysis module from all prophages predicted in all the different Bacterial clades (Table S2), a total of 3,462 prophages. The lysis module is generally located next to the tail module in Firmicute prophages, But adjacent to the packaging (terminase) module in Escherichia phages. 1 Figure S5: Candidate Mu-like prophage in the Negativicute Propionispora vibrioides. Phage-related genes (arrows indicate transcription direction) are coloured and show characteristics of Mu-like genome organization. Figure S6: The genome maps of Negativicute prophages harbouring candidate antiBiotic resistance genes MBL (top three Veillonella prophages) and tet(32) (bottom Selenomonas prophage remnant); excludes the ACI-1 prophage harbouring example characterised previously (Rands et al., 2018).
    [Show full text]
  • Analysis of the Gut Bacterial Communities in Beef Cattle and Their Association with Feed Intake, Growth, and Efficiency1,2,3
    Published online July 13, 2017 Analysis of the gut bacterial communities in beef cattle and their association with feed intake, growth, and efficiency1,2,3 P. R. Myer,*4 H. C. Freetly,† J. E. Wells,† T. P. L. Smith,† and L. A. Kuehn† *Department of Animal Science, University of Tennessee Institute of Agriculture, University of Tennessee, Knoxville 37996; and †USDA5, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933 ABSTRACT: The impetus behind the global food secu- utilization. The use of metagenomics and high-through- rity challenge is direct, with the necessity to feed almost put sequencing has greatly impacted the study of the 10 billion people by 2050. Developing a food-secure ruminant gut. The ability to interrogate these systems at world, where people have access to a safe and sustain- great depth has permitted a greater understanding of the able food supply, is the principal goal of this challenge. microbiological and molecular mechanisms involved To achieve this end, beef production enterprises must in ruminant nutrition and health. Although the micro- develop methods to produce more pounds of animal bial communities of the reticulorumen have been well protein with less. Selection for feed-efficient beef cattle documented to date, our understanding of the popu- using genetic improvement technologies has helped to lations within the gastrointestinal tract as a whole is understand and improve the stayability and longevity limited. The composition and phylogenetic diversity of of such traits within the herd. Yet genetic contributions the gut microbial community are critical to the overall to feed efficiency have been difficult to identify, and well-being of the host and must be determined to fully differing genetics, feed regimens, and environments understand the relationship between the microbiomes among studies contribute to great variation and inter- within segments of the cattle gastrointestinal tract and pretation of results.
    [Show full text]
  • The Role of the Vaginal Microbiome in Distinguishing Female Chronic Pelvic Pain Caused by Endometriosis/Adenomyosis
    771 Original Article Page 1 of 12 The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis Xiaopei Chao1,2, Yang Liu1,2, Qingbo Fan1,2, Honghui Shi1,2, Shu Wang1,2, Jinghe Lang1,2 1Department of Obstetrics and Gynecology, Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China; 2National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China Contributions: (I) Conception and design: S Wang, J Lang; (II) Administrative support: S Wang, Q Fan, H Shi; (III) Provision of study materials or patients: X Chao, Y Liu; (IV) Collection and assembly of data: X Chao, S Wang; (V) Data analysis and interpretation: X Chao, S Wang; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. Correspondence to: Shu Wang; Jinghe Lang. Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Shuaifuyuan No. 1, Dongcheng District, Beijing 100730, China. Email: [email protected]; [email protected]. Background: This study aimed to investigate the specific vaginal microbiome in the differential diagnosis of endometriosis/adenomyosis (EM/AM)-associated chronic pelvic pain (CPP) from other types of CPP, and to explore the role of the vaginal microbiome in the mechanism of EM/AM-associated CPP. Methods: We recruited 37 women with EM/AM-associated CPP, 25 women with chronic pelvic pain syndrome (CPPS) without EM/AM, and 66 women without CPPS into our study. All of the participants were free from human papillomavirus (HPV) infection. Sequencing of barcoded 16S rRNA gene fragments (V4) was used to determine the vaginal microbiome composition on the Illumina HiSeq2500 System.
    [Show full text]
  • Modulation of the Intestinal Microbiota and the Metabolites Produced by the Administration of Ice Cream and a Dietary Supplement Containing the Same Probiotics
    Downloaded from British Journal of Nutrition (2020), 124, 57–68 doi:10.1017/S0007114520000896 https://www.cambridge.org/core © The Authors 2020 Modulation of the intestinal microbiota and the metabolites produced by the administration of ice cream and a dietary supplement containing the same probiotics . IP address: 170.106.202.58 Vivian Cristina da Cruz Rodrigues1, Ana Luiza Rocha Faria Duque2, Luciana de Carvalho Fino1, Fernando Moreira Simabuco1, Adilson Sartoratto3, Lucélia Cabral4, Melline Fontes Noronha5, Katia Sivieri2 and Adriane Elisabete Costa Antunes1* , on 1 School of Applied Sciences (FCA), State University of Campinas, Limeira, SP 13484-350, Brazil 28 Sep 2021 at 07:32:53 2Department of Food and Nutrition, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, SP 14800-903, Brazil 3Division of Organic and Pharmaceutical Chemistry, Pluridisciplinary Center for Chemical, Biological and Agricultural Research (CPQBA), State University of Campinas, Paulínia, SP 13148-218, Brazil 4Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-970, Brazil , subject to the Cambridge Core terms of use, available at 5Genome Research Division, Research Informatics Core, Research Resource Center, University of Illinois at Chicago, Chicago, IL 60612, USA (Submitted 7 November 2019 – Final revision received 13 January 2020 – Accepted 21 February 2020 – First published online 6 March 2020) Abstract The aim of the present work was to compare the capacity to modulate the intestinal microbiota and the production of metabolites after 14 d administration of a commercial dietary supplement and a manufactured ice cream, both containing the same quantity of inulin and the same viable counts of Lactobacillus acidophilus LA-5 and Bifidobacterium animalis BB-12, using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) model.
    [Show full text]